Plot

As a child, Bruce Wayne (Christian Bale) falls into an abandoned well filled with bats, causing him to develop a phobia. Bruce's father Thomas is a rich industrialist and owner of Wayne Enterprises, who built the monorail for Gotham city to provide cheap transportation for the residents of the city. At the opera with his parents, Bruce becomes unsettled by performers masquerading as bats and asks to leave. Outside, mugger Joe Chill murders Bruce's parents in front of him. Bruce is raised by the family butler, Alfred Pennyworth.

14 years later, Chill is granted parole in exchange for agreeing to testify against crime boss Carmine Falcone (Tom Wilkinson). Falcone is the most powerful Mafia boss in Gotham, who shares a prison cell with Joe Chill after he murdered Bruce's parents.

Bruce, now a young man, goes to the courthouse intending to shoot Chill, but one of Falcone's assassins does so first. Bruce confides in his childhood friend Rachel Dawes (Katie Holmes), now a Gotham City district attorney, who is disgusted by Bruce's desire for vengeance. Rachel convinces Bruce that the real enemy in Falcone, who is destroying the city of Gotham and things for the masses are worse than ever. Rachel says that Gotham has no chance of survival if the good people do nothing.

After confronting Falcone, who says real power comes from being feared, Bruce spends the next seven years traveling the world, training in combat, and immersing himself in the criminal underworld. Bruce hopes of learning skills that will allow him to return to Gotham and free it from the crime and corruption that threatens to consume it.

In a Bhutanese prison, he meets Ducard (Liam Neeson), who offers to train him as a ninja of the League of Shadows led by Ra's Al Ghul (Ken Watanabe). Ducard is the leader of the League of Shadows, an ancient society that uses chaos to punish the corrupt and decadent. Ducard tells Bruce the path to get to the HQ of the League of Shadows. Bruce has to climb a grueling and freezing mountain to get to his destination, which is a large castle at the top of the mountain. Ra's Al Ghul tells Bruce that to manipulate the fears of others, he must first learn to master his own fears. Ducard hands Bruce a peculiar blue colored flower, as he asks him about his fears. Bruce is taught to overcome his fear of bats and the overwhelming guilt that he could not avenge his own parents.

As he completes his training, Bruce learns of the League's true intentions: to liberate Gotham from the evils that plague it by destroying the city. Bruce rejects the League and its mandate that killing is necessary. He escapes, burning down their temple in the process. Ra's is killed by falling debris, while Bruce saves the unconscious Ducard.

Bruce returns to Gotham. While publicly posing as a reckless playboy, he takes an interest in his family's company, Wayne Enterprises, a technology and defense conglomerate run by the unscrupulous CEO William Earle (Rutger Hauer), who intends to take the company public.

Bruce meets Lucius Fox (Morgan Freeman), a high-ranking Wayne Enterprises employee demoted to working in the company's Applied Science Division, where he conducts advanced studies in biochemistry and mechanical engineering. Lucius introduces him to several of Wayne's experimental prototype technologies, including an armored car and protective bodysuit, which Bruce uses to form his crime-fighting persona, Batman, inspired by his childhood fear, which he has now conquered.

As Batman, Bruce intercepts an illegal drug shipment, empowering Sgt. Jim Gordon (Gary Oldman) and the Gotham police to arrest the previously untouchable Falcone. Gordon is one of the few Gotham City police officers who is not corrupted, who was on duty the night of the murder of Bruce's parents and, in this way, shares a special bond with the adult Bruce and thus with Batman.

Meanwhile, a Wayne Enterprises cargo ship is raided and an experimental weapon is stolen, a "Microwave Emitter" that uses microwaves to vaporize an enemy's water supply.

Back in Gotham, Falcone and his henchmen are declared mentally unfit for trial and transferred to Arkham Asylum by the corrupt Dr. Jonathan Crane / Scarecrow (Cillian Murphy), who had been using Falcone to import a dangerous hallucinogenic drug that causes severe psychosis.

Crane exposes Falcone to the toxin while wearing a burlap mask, driving Falcone mad with fear of the "Scarecrow." While investigating Crane, Batman is also exposed to the drug and is rescued by Alfred and given an antidote by Fox.

Rachel goes to Arkham, where Crane reveals that he has been dumping the toxin into Gotham's water supply before dosing her with it. She is rescued by Batman, who exposes Crane to the toxin and interrogates him. Crane reveals that the toxin is harmless in liquid form and only dangerous if inhaled. Batman inoculates Rachel and gives her two vials of the antidote, one for Sgt. Gordon and one for mass production.

At his birthday celebration at Wayne Manor, Bruce is confronted by Ducard, who reveals himself to be the real Ra's Al Ghul. Bruce fakes a drunken tirade to get rid of his guests, leaving him alone with Ra's and his ninjas. Ra's reveals the League's plan to destroy Gotham: having stolen the Microwave Emitter and conspired with Crane, they intend to vaporize the city's toxin-riddled water supply, creating mass hysteria and violence.

The League sets fire to the mansion and Bruce is nearly trapped inside but is saved by Alfred (Michael Caine). As the League begins unleashing the toxin, Batman rescues Rachel from a drug-induced mob and reveals his true identity to her. He entrusts Sgt. Gordon with the Batmobile and pursues Ra's, who is using Gotham's train system to deliver the weapon throughout the city. Batman confronts Ra's on the train and escapes just as Gordon uses the Batmobile to destroy the elevated tracks, leaving Ra's to die in the ensuing crash.

Batman becomes a public hero, but simultaneously loses Rachel, who cannot bring herself to love both Bruce and Batman. Bruce buys a controlling stake in the now publicly-traded Wayne Enterprises, fires Earle, and replaces him with Fox. Jim Gordon is promoted to Lieutenant. He shows Batman the new Bat-Signal and mentions a new costumed criminal who leaves Joker cards at crime scenes. Batman promises to investigate, and disappears into the night.